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Editing registered metadata to add confounding variables #642

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oquendoM opened this issue Jun 20, 2024 · 9 comments · May be fixed by #877
Open

Editing registered metadata to add confounding variables #642

oquendoM opened this issue Jun 20, 2024 · 9 comments · May be fixed by #877
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core Feature or fix task considered to be in the core product enhancement New feature or request

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@oquendoM
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oquendoM commented Jun 20, 2024

Is your feature request related to a problem? Please describe.
I would like to be able to add confounding variables to already registered samples.

Describe the solution you'd like
After registration of a batch, it would be nice to be able to add confounding variables (ex. age, sex, BMI, cell culture medium, etc.) when editing the metadata of the batch.

Describe alternatives you've considered
At the moment the information can only be added as a comment, but it would be better to have it as a separate column. The new columns could be added through the browser editing function or, if not possible, by downloading the metadata as txt and uploading it with the additional columns.


Based on personal discussions with @oquendoM @Shraddha0903 and @FraBarSol we conclude some facts and properties for confounding variables in the application:

  • can be categorical or continuous
  • are not always available beforehand
  • can be provided at any point of the project
  • are annotations of samples
  • can be associated based on the sample name and sample id
  • can be incomplete

In the case of an incomplete annotation of samples, warn the user but not block the annotation process. It might be, that there are missing values and the user is aware of it.

The use case

"As a researcher, I want to annotate samples with confounding variables and their value for samples in a batch."

Requirements

  • If at least one sample misses an annotation for a provided confounding variable, warn the user before saving any change
  • The user is given the sample id and sample name during annotation
  • The user can update existing confounding variables
@sven1103
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sven1103 commented Jun 20, 2024

DM-1115

@sven1103 sven1103 added the enhancement New feature or request label Jun 20, 2024
@sven1103
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Dear @oquendoM ,

thank you for your request! The feature is actually already scheduled in the current development sprint and the first draft hopefully soon ready to show.

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github-actions bot commented Aug 2, 2024

This issue is stale because it has been open for 30 days with no activity.

@github-actions github-actions bot added the stale label Aug 2, 2024
@sven1103
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sven1103 commented Aug 5, 2024

Depends on #680, since it would enable us to let the user provide additional columns for confounding variables.

@github-actions github-actions bot removed the stale label Aug 6, 2024
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github-actions bot commented Sep 5, 2024

This issue is stale because it has been open for 30 days with no activity.

@github-actions github-actions bot added the stale label Sep 5, 2024
@sven1103 sven1103 removed the stale label Sep 26, 2024
@sven1103 sven1103 added the core Feature or fix task considered to be in the core product label Sep 26, 2024
@Shraddha0903 Shraddha0903 self-assigned this Sep 26, 2024
@Shraddha0903 Shraddha0903 moved this to In Progress in UI/UX Task list Sep 26, 2024
@KochTobi KochTobi moved this to In Progress in Sprint Planning Oct 22, 2024
@KochTobi KochTobi self-assigned this Oct 22, 2024
@KochTobi KochTobi added the needs clarification Unclear issue where more information needs to be provided by the issuer label Oct 22, 2024
@KochTobi
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We decided to move the concept of sample batches into the confounding variables.

@KochTobi KochTobi removed the needs clarification Unclear issue where more information needs to be provided by the issuer label Oct 28, 2024
@KochTobi
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Samples within one experiment share experimental and confounding variables even if there is no value for some samples.

@KochTobi KochTobi linked a pull request Oct 30, 2024 that will close this issue
@KochTobi
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KochTobi commented Oct 30, 2024

For context: The confounding variables may later be used for analysis. By filtering data for samples with certain criteria in confounding variables, effects of these variables on the results are investigated.

@KochTobi KochTobi linked a pull request Nov 4, 2024 that will close this issue
@Shraddha0903 Shraddha0903 moved this from In Progress to Done in UI/UX Task list Nov 12, 2024
KochTobi added a commit that referenced this issue Nov 26, 2024
…etadata-to-add-confounding-variables

# Conflicts:
#	user-interface/src/main/bundles/dev.bundle
KochTobi added a commit that referenced this issue Nov 27, 2024
KochTobi added a commit that referenced this issue Nov 28, 2024
KochTobi added a commit that referenced this issue Nov 29, 2024
…etadata-to-add-confounding-variables

# Conflicts:
#	user-interface/src/main/bundles/dev.bundle
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This issue is stale because it has been open for 30 days with no activity.

@github-actions github-actions bot added the stale label Nov 30, 2024
@KochTobi KochTobi removed the stale label Dec 3, 2024
KochTobi added a commit that referenced this issue Dec 10, 2024
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Labels
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4 participants